Dear Roman, I confirm that the Topology is not always -1 at endpoints. There is an explanation for this (which doesn't mean the current state makes sense, only that it's not a random bug): the algorithm chops the network with a sphere acting like a PacMan (it doesn't actually chop it for efficiency, but that's the idea). When the sphere "sees" a new profile (the intersection between the sphere and the surface), then walks to it and chops again, when it sees more than one new profile it generates a bifurcation, when it sees no new profiles it stops and assigns a -1 topology to the last network point.
Now, at a later step, the network is cleaned up, meaning that very short, lateral segments that end with a -1 topology are removed (these might originate from surface irregularities). At the time of writing the algorithm, I preferred to keep the topology information unchanged so that an uncleaned and a cleaned-up network contained as much of the same information as possible. Now I see that it would probably be good to have a -1 topology as one would expect without knowing all the above. It will go in the next release, in the meantime you can rely on the fact that a point at the end of a segment is only used by one cell. Alternatively, let me know if you usually compile vmtk from source, so that you could benefit from an early fix. Best, Luca On Sep 18, 2012, at 3:28 PM, Dr. Roman Grothausmann wrote: > Dear Luca, > > > Thanks for Your reply. > > On 18/09/12 11:47, Luca Antiga wrote: >> Hi Roman, >> I'm not sure, it could be the fact that Paraview shows cell-based data by >> coloring the whole cell with a uniform color, but it may also be that there's >> a bug with setting topology values somewhere. >> Can you share the network file so that I can take a direct look? > > Sure, it's attached. > > Many thaks for looking into this. > Roman > > >> On Sep 14, 2012, at 3:26 PM, Dr. Roman Grothausmann wrote: >> >>> On 03/09/12 11:39, Luca Antiga wrote: >>>> Dear Roman, >>>> thanks for your appreciation of vmtk, it's good to have you onboard. >>>> >>>> It is indeed possible to use manually specified endpoints for >>>> vmtkcenterlines, >>>> but there's some glue code that needs to be written in-between. >>>> >>>> vmtknetworkextraction outputs a polydata dataset composed of interconnected >>>> lines, whose endpoints are the coordinates you're interested in. In order >>>> to >>>> extract endpoints from the Network you should look for cells that have >>>> either >>>> one of the Topology array values equal to -1 and extract the corresponding >>>> coordinates. >>> >>> I tried to check this with paraview and its python-calculator using: >>> (Topology[:,0] +1) * (Topology[:,1] +1) and colouring the result with a >>> colour range from 0 to 1 (blue to red, see screen shot). It seems not all >>> cells containing endpoints have one of the topology values == -1, or have I >>> done something wrong? >>> >>> Thanks for any help or hints >>> Roman >>> >>>> >>>> Once you have the coordinates, you can specify them even at the command >>>> line using vmtkcenterlines using -seedselector pointlist -seeds x y z >>>> -targets x0 y0 z0 x1 y1 z1 ... >>>> >>>> Let me know if you need support/advice for the extraction of the >>>> endpoints. In >>>> fact this could be a nice addition to vmtk. >>>> >>>> Best, >>>> >>>> >>>> Luca >>>> >>>> >>>> On Sep 3, 2012, at 11:26 AM, Dr. Roman Grothausmann wrote: >>>> >>>>> Dear mailing list members, >>>>> >>>>> >>>>> vmtk is really cool. I'm just about getting to know its features >>>>> especially those for centre line extraction. >>>>> I found this email from Luca: >>>>> http://sourceforge.net/mailarchive/message.php?msg_id=29119553 to use >>>>> vmtknetworkextraction for this purpose. >>>>> >>>>> Now I wonder, if it is possible to use the endpoints of the result of >>>>> vmtknetworkextraction as the endpoints for vmtkcenterlines? >>>>> Or is there a way to save the manually selected start and end points of >>>>> vmtkcenterlines to use these when experimenting with other options of >>>>> vmtkcenterlines? >>>>> >>>>> Many thanks for vmtk and for any help or hints. >>>>> Roman >>>>> >>>>> -- >>>>> Dr. Roman Grothausmann >>>>> >>>>> Tomographie und Digitale Bildverarbeitung >>>>> Tomography and Digital Image Analysis >>>>> >>>>> Institut für Funktionelle und Angewandte Anatomie, OE 4120 >>>>> Medizinische Hochschule Hannover >>>>> Carl-Neuberg-Str. 1 >>>>> 30625 Hannover >>>>> >>>>> Tel. +49 511 532-9574 >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Live Security Virtual Conference >>>>> Exclusive live event will cover all the ways today's security and >>>>> threat landscape has changed and how IT managers can respond. Discussions >>>>> will include endpoint security, mobile security and the latest in malware >>>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>>>> _______________________________________________ >>>>> vmtk-users mailing list >>>>> vmtk-users@lists.sourceforge.net >>>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users >>>> >>> >>> -- >>> Dr. Roman Grothausmann >>> >>> Tomographie und Digitale Bildverarbeitung >>> Tomography and Digital Image Analysis >>> >>> Institut für Funktionelle und Angewandte Anatomie, OE 4120 >>> Medizinische Hochschule Hannover >>> Carl-Neuberg-Str. 1 >>> 30625 Hannover >>> >>> Tel. +49 511 532-9574 >>> <endpoints.jpg>------------------------------------------------------------------------------ >>> Got visibility? >>> Most devs has no idea what their production app looks like. >>> Find out how fast your code is with AppDynamics Lite. >>> http://ad.doubleclick.net/clk;262219671;13503038;y? >>> http://info.appdynamics.com/FreeJavaPerformanceDownload.html_______________________________________________ >>> vmtk-users mailing list >>> vmtk-users@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/vmtk-users >> > > -- > Dr. Roman Grothausmann > > Tomographie und Digitale Bildverarbeitung > Tomography and Digital Image Analysis > > Institut für Funktionelle und Angewandte Anatomie, OE 4120 > Medizinische Hochschule Hannover > Carl-Neuberg-Str. 1 > 30625 Hannover > > Tel. +49 511 532-9574 > <Bronc01_bi4_p1_c-open_nw.vtp>------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. > http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________ > vmtk-users mailing list > vmtk-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/vmtk-users ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ vmtk-users mailing list vmtk-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/vmtk-users
